IKK-β proteins, nucleic acids and methods

ABSTRACT

The invention provides methods and compositions relating to an IκB kinase, IKK-β, and related nucleic acids. The polypeptides may be produced recombinantly from transformed host cells from the disclosed IKK-β encoding nucleic acids or purified from human cells. The invention provides isolated IKK-β hybridization probes and primers capable of specifically hybridizing with the disclosed IKK-β genes, IKK-β-specific binding agents such as specific antibodies, and methods of making and using the subject compositions in diagnosis, therapy and in the biopharmaceutical industry.

This is a divisional application of U.S. Ser. No. 08/890,853, filed Jul. 10, 1997, now U.S. Pat. No. 5,851,812, which is a continuing application under 35USC120 of U.S. Ser. No. 08/887,114 filed Jul. 1, 1997, abandoned, both of which are incorporated herein by reference.

FIELD OF THE INVENTION

The field of this invention is proteins involved in transcription factor activation.

BACKGROUND

Cytokines trigger changes in gene expression by modifying the activity of otherwise latent transcription factors (Hill and Treisman, 1995). Nuclear factor κB (NF-κB) is a prominent example of how such an external stimulus is converted into an active transcription factor (Verma et al., 1995). The NF-κB system is composed of homo- and heterodimers of members of the Rel family of related transcription factors that control the expression of numerous immune and inflammatory response genes as well as important viral genes (Lenardo and Baltimore, 1989; Baeuerle and Henkel, 1994). The activity of NP-κB transcription factors is regulated by their subcellular localization (Verma et al., 1995). In most cell types, NF-κB is present as a heterodimer comprising of a 50 kDa and a 65 kDa subunit. This heterodimer is sequestered in the cytoplasm in association with IκBα a member of the IκB family of inhibitory proteins (Finco and Baldwin, 1995; Thanos and Maniatis, 1995; Verma et al., 1995). IκBα masks the nuclear localization signal of NF-κB and thereby prevents NF-κB nuclear translocation. Conversion of NF-κB into an active transcription factor that translocates into the nucleus and binds to cognate DNA sequences requires the phosphorylation and subsequent ubiquitin-dependent degradation of IκBα in the 26 s proteasome. Signal-induced phosphorylation of IκBα occurs at serines 32 and 36. Mutation of one or both of these serines renders IκBα resistant to ubiquitination and proteolytic degradation (Chen et al., 1995); DiDonato, 1996 #370, Roff, 1996 #397.

The pleiotropic cytokines tumor necrosis factor (TNF) and interleukin-1 (IL-1) are among the physiological inducers of IκB phosphorylation and subsequent NF-κB activation (Osborn et al., 1989; Beg et al., 1993). Although TNF and IL-1 initiate signaling cascades leading to NF-κB activation via distinct families of cell-surface receptors (Smith et al., 1994; Dinarello, 1996), both pathways utilize members of the TNF receptor-associated factor (TRAF) family of adaptor proteins as signal transducers (Rothe et al., 1995; Hsu et al., 1996; Cao et al., 1996b). TRAF proteins were originally found to associate directly with the cytoplasmic domains of several members of the TNF receptor family including the 75 kDa TNF receptor (TNFR2), CD40, CD30, and the lymphotoxin-β receptor (Rothe et al., 1994; Hu et al., 1994; Cheng et al., 1995; Mosialos et al., 1995; Song and Donner, 1995; Sato et al., 1995; Lee et al., 1996; Gedrich et al., 1996; Ansieau et al., 1996). In addition, TRAF proteins are recruited indirectly to the 55 kDa TNF receptor (TNFR1) by the adaptor protein TRADD (Hsu et al., 1996). Activation of NF-κB by TNF requires TRAF2 (Rothe et al., 1995; Hsu et al., 1996). TRAF5 has also been implicated in NF-κB activation by members of the TNF receptor family (Nakano et al., 1996); 1996 #240. In contrast, TRAF6 participates in NF-κB activation by IL-1 (Cao et al., 1996b). Upon IL-1 treatment, TRAF6 associates with IRAK, a serine-threonine kinase that binds to the IL-1 receptor complex (Cao et al., 1996a); Huang, 1997.

The NF-κB-inducing kinase (NIK) is a member of the MAP kinase kinase kinase (MAP3K) family that was identified as a TRAF2-interacting protein (Malinin et al., 1997). NIK activates KF-κB when overexpressed, and kinase-inactive mutants of NIK comprising its TRAF2-interacting C-terminal domain (NIK.sub.(624-947)) or lacking two crucial lysine residues in its kinase domain (NIK.sub.(KK429-430AA)) behave as dominant-negative inhibitors that suppress TNF-, IL-1-, and TRAF2-induced NF-κB activation (Malinin et al., 1997). Recently, NIK was found to associate with additional members of the TRAF family, including TRAF5 and TRAF6. Catalytically inactive mutants of NIK also inhibited TRAF5- and TRAF6-induced NF-κB activation, thus providing a unifying concept for NIK as a common mediator in the NF-κB signaling cascades triggered by TNF and IL-1 downstream of TRAFs.

Here, we disclose a novel kinase IκB Kinase, IKK-β, as a NIK-interacting protein. IKK-β has sequence similarity to the conceptual translate of a previously identified open reading frame postulated to encode a serine-threonine kinase of unknown function (`Conserved Helix-loop-helix Ubiquitous Kinase` or CHUK, Connelly and Marcu, 1995; Mock et al., 1995). Catalytically inactive mutants of IKK-β are shown to suppress NF-κB activation induced by TNF and IL-1 stimulation as well as by TRAF and NIK overexpression; transiently expressed IKK-β is shown to associate with the endogenous IκBα complex; and IKK-β is shown to phosphorylate IκBα on serines 32 and 36. As used herein, Ser32 and Ser36 of IκB refers collectively to the two serine residues which are part of the consensus sequence DSGL/IXSMIL (e.g. ser 32 and 36 in IκBα, ser 19 and 23 in I-κBβ, and ser 157 and 161, or 18 and 22, depending on the usage of methionines, in IκBε, respectively.

SUMMARY OF THE INVENTION

The invention provides methods and compositions relating to isolated IKK-β polypeptides, related nucleic acids, polypeptide domains thereof having IKK-β-specific structure and activity and modulators of IKK-β function, particularly IκB kinase activity. IKK-β polypeptides can regulate NFκB activation and hence provide important regulators of cell function. The polypeptides may be produced recombinantly from transformed host cells from the subject IKK-β polypeptide encoding nucleic acids or purified from mammalian cells. The invention provides isolated IKK-β hybridization probes and primers capable of specifically hybridizing with the disclosed IKK-β gene, IKK-β-specific binding agents such as specific antibodies, and methods of making and using the subject compositions in diagnosis (e.g. genetic hybridization screens for IKK-β transcripts), therapy (e.g. IKK-β kinase inhibitors to inhibit TNF signal transduction) and in the biopharmaceutical industry (e.g. as immunogens, reagents for isolating other transcriptional regulators, reagents for screening chemical libraries for lead pharmacological agents, etc.).

DETAILED DESCRIPTION OF THE INVENTION

The nucleotide sequence of a natural cDNA encoding a human IKK-β polypeptide is shown as SEQ ID NO: 1, and the full conceptual translate is shown as SEQ ID NO:2. The IKK-β polypeptides of the invention include incomplete translates of SEQ ID NO: 1 and deletion mutants of SEQ ID NO:2, which translates and deletion mutants have IKK-β-specific amino acid sequence and binding specificity or function.

The IKK-β polypeptide domains of the invention have amino acid sequences distinguishable from IKK-α, generally at least 11, preferably at least 21, more preferably at least 31 consecutive residues of SEQ ID NO:2 and provide IKK-β domain specific activity or function, such as IKK-β-specific kinase or kinase inhibitory activity, NIK-binding or binding inhibitory activity, IκB-binding or binding inhibitory activity, NFκB activating or inhibitory activity or antibody binding. Preferred domains phosphorylate at least one and preferably both the serine 32 and 36 of IκB (Verma, I. M., et al. (1995)).

IKK-β-specific activity or function may be determined by convenient in vitro, cell-based, or in vivo assays: e.g. in vitro binding assays, cell culture assays, in animals (e.g. gene therapy, transgenics, etc.), etc. Binding assays encompass any assay where the molecular interaction of an IKK-β polypeptide with a binding target is evaluated. The binding target may be a natural intracellular binding target such as an IKK-β substrate, a IKK-β regulating protein or other regulator that directly modulates IKK-β activity or its localization; or non-natural binding target such a specific immune protein such as an antibody, or an IKK-β specific agent such as those identified in screening assays such as described below. IKK-β-binding specificity may assayed by kinase activity or binding equilibrium constants (usually at least about 10⁷ M⁻¹, preferably at least about 10⁸ M⁻¹, more preferably at least about 10⁹ M⁻¹), by the ability of the subject polypeptide to function as negative mutants in IKK-β-expressing cells, to elicit IKK-β specific antibody in a heterologous host (e.g a rodent or rabbit), etc. In any event, the IKK-β binding specificity of the subject IKK-β polypeptides necessarily distinguishes IKK-α (SEQ ID NO:4).

The claimed IKK-β polypeptides are isolated or pure: an "isolated" polypeptide is unaccompanied by at least some of the material with which it is associated in its natural state, preferably constituting at least about 0.5%, and more preferably at least about 5% by weight of the total polypeptide in a given sample and a pure polypeptide constitutes at least about 90%, and preferably at least about 99%. by weight of the total polypeptide in a given sample. The IKK-β polypeptides and polypeptide domains may be synthesized, produced by recombinant technology, or purified from mammalian, preferably human cells. A wide variety of molecular and biochemical methods are available for biochemical synthesis, molecular expression and purification of the subject compositions, see e.g. Molecular Cloning, A Laboratory Manual (Sambrook, et al. Cold Spring Harbor Laboratory), Current Protocols in Molecular Biology (Eds. Ausubel, et al., Greene Publ. Assoc., Wiley-Interscience, NY) or that are otherwise known in the art.

The invention provides binding agents specific to the subject kinase proteins including substrates, agonists, antagonists, natural intracellular binding targets, etc., methods of identifying and making such agents, and their use in diagnosis, therapy and pharmaceutical development. For example, specific binding agents are useful in a variety of diagnostic and therapeutic applications, especially where disease or disease prognosis is associated with improper utilization of a pathway involving the subject proteins, e.g. NF-κB activation. Novel IKK-β-specific binding agents include IKK-β-specific receptors, such as somatically recombined polypeptide receptors like specific antibodies or T-cell antigen receptors (see, e.g Harlow and Lane (1988) Antibodies, A Laboratory Manual, Cold Spring Harbor Laboratory) and other natural intracellular binding agents identified with assays such as one-, two- and three-hybrid screens, non-natural intracellular binding agents identified in screens of chemical libraries such as described below, etc. Agents of particular interest modulate IKK-β function, e.g. IKK-β-dependent transcriptional activation. For example, a wide variety of inhibitors of IKK-β IκB kinase activity may be used to regulate signal transduction involving IκB. Exemplary IKK-β IκB kinase inhibitors include known classes of serine/threonine kinase (e.g. PKC) inhibitors such as competitive inhibitors of ATP and substrate binding, antibiotics, IKK-β-derived peptide inhibitors, etc., see Tables 1 and 2. IKK-β specificity and activity are readily quantified in high throughput kinase assays using panels of protein kinases (see cited references and Examples).

Preferred inhibitors include natural compounds such as staurosporine (Omura S, et al. J Antibiot (Tokyo) 1995 Jul;48(7):535-48), produced by a marine organism, and synthetic compounds such as PD 153035, which also potently inhibits the EGF receptor protein kinase (Fry D. W. et al. Science 1994 Aug 19;265(5175):1093-5). Members of the tyrphostin family of synthetic protein kinase inhibitors are also useful; these include compounds which are pure ATP competitors, compounds which are pure substrate competitors, and compounds which are mixed competitors: compete with both ATP and substrate (Levitzki A and Gazit A, Science 1995 Mar 24;267(5205):1782-8). Additional IKK-β inhibitors include peptide-based substrate competitors endogenously made by the mammalian cell, e.g. PKI (protein kinase inhibitor, Seasholtz AF et al., Proc Natl Acad Sci USA 1995 Feb 28;92(5):1734-8 ), or proteins inhibiting cdc kinases (Correa-Bordes J and Nurse P, Cell 1995 Dec 15;83(6):1001-9). Additional small peptide based substrate competitive kinase inhibitors and allosteric inhibitors (inhibitory mechanisms independent of ATP or substrate competition) are readily generated by established methods (Hvalby 0, et al. Proc Natl Acad Sci USA 1994 May 24;91(11):4761-5; Barja P, et al., Cell Immunol 1994 Jan;153(1):28-38; Villar-Palasi C, Biochim Biophys Acta 1994 Dec 30;1224(3):384-8; Liu W. Z., et al., Biochemistry 1994 Aug 23;33(33):10120-6).

                  TABLE I     ______________________________________     Selected Small Molecule IKK-β Kinase Inhibitors     Inhibitors  Citations     ______________________________________     HA-100.sup.1                 1. Hagiwara, M,. et al. Mol. Pharmacol.                 32: 7 (1987)     Chelerythrine.sup.2                 2. Herbert, J. M., et al. Biochem Biophys                 Res Com 172: 993 (1990)     Staurosporine.sup.3,4,5                 3. Schachtele, C., et al. Biochem Biophys                 Res Com 151: 542 (1988)     Calphostin C.sup.6,7,8,9                 4. Tamaoki, T., et al. Biochem Biophys                 Res Com 135: 397 (1986)     K-252b.sup.10                 5. Tischler, A. S., et al. J. Neurochemistry 55:                 1159 (1990)     PKC 19-36.sup.11                 6. Bruns, R. F., et al. Biochem Biophys                 Res Com 176: 288 (1991)     Iso-H7.sup.12                 7. Kobayashi, E., et al. Biochem Biophys                 Res Com 159: 548 (1989)     PKC 19-31   8. Tamaoki, T., et al Adv2nd Mass                 Phosphoprotein Res 24: 497 (1990)     H-7.sup.13,3,14                 9. Tamaoki, T., et al. Biotechnology                 8: 732 (1990)     H-89.sup.15 10. Yasuzawa, T. J. Antibiotics 39: 1972 (1986)     KT5720.sup.16                 11. House, C., et al. Science 238: 1726 (1987)     cAMP-depPKinhib.sup.17                 12. Quick, J., et al. Biochem. Biophys.                 Res. Com. 167: 657 (1992)     A-3.sup.18  13. Bouli, N. M. and Davis, M. Brain                 Res. 525: 198 (1990)     HA1004.sup.19,20                 14. Takahashi, I., et al. J. Pharmacol. Exp.                 Ther. 255: 1218 (1990)     K-252a.sup.16,5                 15. Chijiwa, T., et al. J. Biol. Chem.                 265: 5267 (1990)     KT5823.sup.16                 16. Kase, H., et al. Biochem. Biophys.                 Res. Com. 142: 436 (1987)     ML-9.sup.21 17. Cheng, H. C., et al. J. Biol. Chem.                 261: 989 (1986)     KT5926.sup.22                 18. Inagaki, M., et al. Mol. Pharmacol.                 29: 577 (1986)                 19. Asano, T. and Hidaka, H. J Pharmaco.                 Exp Ther 231: 141 (1984)                 20. Hidaka, H., et al. Biochemistry                 23: 5036 (1984)                 21. Nagatsu, T., et al. Biochem Biophys                 Res Com 143: 1045 (1987)                 22. Nakanishi, S., et al. Mol. Pharmacol.                 37: 482 (1990)     ______________________________________

                  TABLE II     ______________________________________     Selected Peptidyl IKK-β Kinase Inhibitors     ______________________________________     hIκBα, residues 24-39, 32Ala                           hIKK-β, Δ5-203     hIκBα, residues 29-47, 36Ala                           hIKK-β, Δ1-178     hIκBα, residues 26-46, 32/36Ala                           hIKK-β, Δ368-756     hIκBβ, residues 25-38, 32Ala                           hIKK-β, Δ460-748     hIκBβ, residues 30-41, 36Ala                           hIKK-α, Δ1-289     hIκBβ, residues 26-46, 32/36Ala                           hIKK-α, Δ12-219     hIκBε, residues 24-40, 32Ala                           hIKK-α, Δ307-745     hIκBε, residues 31-50, 36Ala                           hIKK-α, Δ319-644     hIκBε, residues 27-44, 32/36Ala     ______________________________________

Accordingly, the invention provides methods for modulating signal transduction involving IκB in a cell comprising the step of modulating IKK-β kinase activity, e.g. by contacting the cell with a serine/threonine kinase inhibitor. The cell may reside in culture or in situ, i.e. within the natural host. Preferred inhibitors are orally active in mammalian hosts. For diagnostic uses, the inhibitors or other IKK-β binding agents are frequently labeled, such as with fluorescent, radioactive, chemiluminescent, or other easily detectable molecules, either conjugated directly to the binding agent or conjugated to a probe specific for the binding agent.

The amino acid sequences of the disclosed IKK-β polypeptides are used to back-translate IKK-β polypeptide-encoding nucleic acids optimized for selected expression systems (Holler et al. (1993) Gene 136, 323-328; Martin et al. (1995) Gene 154, 150-166) or used to generate degenerate oligonucleotide primers and probes for use in the isolation of natural IKK-β-encoding nucleic acid sequences ("GCG" software, Genetics Computer Group, Inc, Madison, Wis.). IKK-β-encoding nucleic acids used in IKK-β-expression vectors and incorporated into recombinant host cells, e.g. for expression and screening, transgenic animals, e.g. for functional studies such as the efficacy of candidate drugs for disease associated with IKK-β-modulated cell function, etc.

The invention also provides nucleic acid hybridization probes and replication/amplification primers having a IKK-β cDNA specific sequence contained in SEQ ID NO:1 and sufficient to effect specific hybridization thereto (i.e. specifically hybridize with SEQ ID NO:1 in the presence of IKK-α cDNA, SEQ ID NO:3). Such primers or probes are at least 12, preferably at least 24, more preferably at least 36 and most preferably at least 96 bases in length. Demonstrating specific hybridization generally requires stringent conditions, for example, hybridizing in a buffer comprising 30% formamide in 5×SSPE (0.18M NaCl, 0.01M NaPO₄, pH7.7, 0.001M EDTA) buffer at a temperature of 42° C. and remaining bound when subject to washing at 42° C. with 0.2×SSPE; preferably hybridizing in a buffer comprising 50% formamide in 5×SSPE buffer at a temperature of 42° C. and remaining bound when subject to washing at 42° C. with 0.2×SSPE buffer at 42° C. IKK-β nucleic acids can also be distinguished using alignment algorithms, such as BLASTX (Altschul et al. (1990) Basic Local Alignment Search Tool, J Mol Biol 215, 403-410).

The subject nucleic acids are of synthetic/non-natural sequences and/or are isolated, i.e. unaccompanied by at least some of the material with which it is associated in its natural state, preferably constituting at least about 0.5%, preferably at least about 5% by weight of total nucleic acid present in a given fraction, and usually recombinant, meaning they comprise a non-natural sequence or a natural sequence joined to nucleotide(s) other than that which it is joined to on a natural chromosome. Recombinant nucleic acids comprising the nucleotide sequence of SEQ ID NO:1 or fragments thereof, contain such sequence or fragment at a terminus, immediately flanked by a sequence other than that which it is joined to on a natural chromosome, or flanked by a native flanking region fewer than 10 kb, preferably fewer than 2 kb, which is at a terminus or is immediately flanked by a sequence other than that which it is joined to on a natural chromosome. While the nucleic acids are usually RNA or DNA, it is often advantageous to use nucleic acids comprising other bases or nucleotide analogs to provide modified stability, etc.

The subject nucleic acids find a wide variety of applications including use as translatable transcripts, hybridization probes, PCR primers, diagnostic nucleic acids, etc.; use in detecting the presence of IKK-β genes and gene transcripts and in detecting or amplifying nucleic acids encoding additional IKK-β homologs and structural analogs. In diagnosis, IKK-β hybridization probes find use in identifying wild-type and mutant IKK-β alleles in clinical and laboratory samples. Mutant alleles are used to generate allele-specific oligonucleotide (ASO) probes for high-throughput clinical diagnoses. In therapy, therapeutic IKK-β nucleic acids are used to modulate cellular expression or intracellular concentration or availability of active IKK-β.

The invention provides efficient methods of identifying agents, compounds or lead compounds for agents active at the level of a IKK-β modulatable cellular function. Generally, these screening methods involve assaying for compounds which modulate IKK-β interaction with a natural IKK-β binding target, in particular, IKK-β phosphorylation of IκB-derived substrates, particularly IκB and NIK substrates. A wide variety of assays for binding agents are provided including labeled in vitro protein-protein binding assays, immunoassays, cell based assays, etc. The methods are amenable to automated, cost-effective high throughput screening of chemical libraries for lead compounds. Identified reagents find use in the pharmaceutical industries for animal and human trials; for example, the reagents may be derivatized and rescreened in in vitro and in vivo assays to optimize activity and minimize toxicity for pharmaceutical development.

In vitro binding assays employ a mixture of components including an IKK-β polypeptide, which may be part of a fusion product with another peptide or polypeptide, e.g. a tag for detection or anchoring, etc. The assay mixtures comprise a natural intracellular IKK-β binding target. In a particular embodiment, the binding target is a substrate comprising IκB serines 32 and/or 36. Such substrates comprise a IκBα, β or ε peptide including the serine 32 and/or 36 residue and at least 5, preferably at least 10, and more preferably at least 20 naturally occurring immediately flanking residues on each side (e.g. for serine 36 peptides, residues 26-46, 22-42, or 12-32 or 151-171 for IκBα,β or ε-derived substrates, respectively). While native full-length binding targets may be used, it is frequently preferred to use portions (e.g. peptides) thereof so long as the portion provides binding affinity and avidity to the subject IKK-β polypeptide conveniently measurable in the assay. The assay mixture also comprises a candidate pharmacological agent. Candidate agents encompass numerous chemical classes, though typically they are organic compounds; preferably small organic compounds and are obtained from a wide variety of sources including libraries of synthetic or natural compounds. A variety of other reagents may also be included in the mixture. These include reagents like ATP or ATP analogs (for kinase assays), salts, buffers, neutral proteins, e.g. albumin, detergents, protease inhibitors, nuclease inhibitors, antimicrobial agents, etc. may be used.

The resultant mixture is incubated under conditions whereby, but for the presence of the candidate pharmacological agent, the IKK-β polypeptide specifically binds the cellular binding target, portion or analog with a reference binding affinity. The mixture components can be added in any order that provides for the requisite bindings and incubations may be performed at any temperature which facilitates optimal binding. Incubation periods are likewise selected for optimal binding but also minimized to facilitate rapid, high-throughput screening.

After incubation, the agent-biased binding between the IKK-β polypeptide and one or more binding targets is detected by any convenient way. For IKK-β kinase assays, `binding` is generally detected by a change in the phosphorylation of a IKK-β substrate. In this embodiment, kinase activity may quantified by the transfer to the substrate of a labeled phosphate, where the label may provide for direct detection as radioactivity, luminescence, optical or electron density, etc. or indirect detection such as an epitope tag, etc. A variety of methods may be used to detect the label depending on the nature of the label and other assay components, e.g. through optical or electron density, radiative emissions, nonradiative energy transfers, etc. or indirectly detected with antibody conjugates, etc.

A difference in the binding affinity of the IKK-β polypeptide to the target in the absence of the agent as compared with the binding affinity in the presence of the agent indicates that the agent modulates the binding of the IKK-β polypeptide to the IKK-β binding target. Analogously, in the cell-based assay also described below, a difference in IKK-β-dependent transcriptional activation in the presence and absence of an agent indicates the agent modulates IKK-β function. A difference, as used herein, is statistically significant and preferably represents at least a 50%, more preferably at least a 90% difference.

The following experimental section and examples are offered by way of illustration and not by way of limitation.

EXPERIMENTAL

Identification of IKK-β

To investigate the mechanism of NIK-mediated NF-κB activation, we initially identified proteins that associate directly with NIK by yeast two-hybrid protein interaction cloning (Fields and Song, 1989). An expression vector was generated that encodes NIK fused to the DNA-binding domain of the yeast transcription factor GAL4. This vector was used as bait in a two-hybrid screen of a human B cell cDNA library. From approximately six million transformants, eight positive clones were obtained, as determined by activation of his and lacZ reporter genes. Of these clones, three encoded a member of the TRAF family, TRAF3 (Hu et al., 1994; Cheng et al., 1995; Mosialos et al., 1995; Sato et al., 1995) and one encoded a novel protein we call IKK-α. Retransformation into yeast cells verified the interaction between NIK and IKK-α. A full-length human IKK-α clone was isolated by screening a Jurkat cDNA library with a probe generated from the 5'-end of the IKK-a two-hybrid clone. IKK-α comprises an N-terminal serine-threonine kinase catalytic domain, a C-terminal helix-loop-helix domain and a leucine zipper-like amphipathic α-helix juxtaposed in between the helix-loop-helix and kinase domain.

To identify potential IKK-α-related genes, we searched a public database of human expressed sequence tags (ESTs). We identified two ESTs (W68756 and AA128064), which we determined were capable of encoding distinct peptides with sequence similarity with IKK-α. IKK-α-related cDNA was cloned by probing a Jurkat cDNA library (human T cell) with an oligonucleotide probe corresponding to sequence from one of the ESTs. Sequence analysis demonstrated that the two ESTs included different fragments of the same gene. The longest cDNA clones obtained had a ˜3.2 kb insert (SEQ ID NO:1) and an open reading frame of 756 amino acids (SEQ ID NO:2). We have designed the protein encoded by this cDNA as IKK-β.

Interaction of IKK-β and NIK in Human Cells

The interaction of IKK-β with NIK was confirmed in mammalian cell coimmunoprecipitation assays. Human IKK-β containing an C-terminal Flag epitope tag was transiently coexpressed in 293 human embryonic kidney cells with Myc epitope-tagged NIK. Cell lysates were immunoprecipitated using a monoclonal antibody against the Flag epitope, and coprecipitating NIK was detected by immunoblot analysis with an anti-Myc monoclonal antibody. In this assay, IKK-β was able to coprecipitate NIK confirming the interaction between both proteins as detected for IKK-α by yeast two-hybrid analysis. Also, a deletion mutant IKK-β protein lacking most of the N-terminal kinase domain (IKK-β.sub.(Δ5-203, i.e., 1-4 & 204-756)) was able to associate with NIK, indicating that the α-helical C-terminal half of IKK-β mediates the interaction with NIK.

Effect of IKK-β and IKK-β Mutants on NF-κB Activation

To investigate a possible role for IKK-β in NF-κB activation, we examined if transient overexpression of IKK-β might activate an NF-κB-dependent reporter gene. An E-selectin-luciferase reporter construct (Schindler and Baichwal, 1994) and a IKK-β expression vector were cotransfected into HeLa cells. IKK-β expression activated the reporter gene in a dose-dependent manner, with a maximal induction of luciferase activity of about 20-fold compared to vector control. Similar results were obtained in 293 cells, where IKK-β overexpression induced reporter gene activity approximately 20-fold. Thus, IKK-β induces NF-κB activation when overexpressed.

We next determined the effect of overexpression of kinase-inactive IKK-β.sub.(Δ5-203) that still associates with NIK on signal-induced NF-κB activation in reporter gene assays in 293 cells. Overexpression of IKK-β.sub.(Δ5-203) blocked TNF- and IL-1-induced reporter gene activation similar to overexpression of NIK.sub.(624-947). IKK-β.sub.(Δ5-203) was also found to inhibited NF-κB-dependent reporter gene activity elicited by overexpression of TRAF2, TRAF6 and NIK. Taken together these results demonstrate that a catalytically inactive IKK-β mutant is a dominant-negative inhibitor of TNF-, IL-1, TRAF- and NIK-induced NF-κB activation. This indicates that IKK-β functions as a common mediator of KF-κB activation by TNF and IL-1 downstream of NIK.

Parenthetical References

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EXAMPLES

1. Protocol for at IKK-β--IκBα phosphorylation assay

A. Reagents

Neutralite Avidin: 20 μg/ml in PBS.

kinase: 10⁻⁸ -10⁻⁵ M IKK-β (SEQ ID NO:2) at 20 μg/ml in PBS.

substrate: 10⁻⁷⁸ -10⁻⁴ M biotinylated substrate (21 residue peptide consisting of residues 26-46 of human IκBα) at 40 μg/ml in PBS.

Blocking buffer: 5% BSA, 0.5% Tween 20 in PBS; 1 hour at room temperature.

Assay Buffer: 100 mM KCl, 10 MM, MgCl₂, 1 mM MnCl₂, 20 mM HEPES pH 7.4, 0.25 mM EDTA, 1% glycerol, 0.5% NP-40, 50 mM BME, 1 mg/ml BSA, cocktail of protease inhibitors.

³² P!γ-ATP 10× stock: 2×10⁻⁵ M cold ATP with 100 μCi ³² P!γ-ATP. Place in the 4° C. microfridge during screening.

Protease inhibitor cocktail (1000×): 10 mg Trypsin Inhibitor (BMB #109894), 10 mg Aprotinin (BMB #236624), 25 mg Benzamidine (Sigma #B-6506), 25 mg Leupeptin (BMB #1017128), 10 mg APMSF (BMB #917575), and 2 mM NaVo₃ (Sigma #S-6508) in 10 ml of PBS.

B. Preparation of assay plates

Coat with 120 μl of stock N Avidin per well overnight at 4° C.

Wash 2 times with 200 μl PBS.

Block with 150 μl of blocking buffer.

Wash 2 times with 200 μl PBS.

C. Assay

Add 40 μl assay buffer/well.

Add 40 μl biotinylated substrate (2-200 pmoles/40 ul in assay buffer)

Add 40 μl kinase (0.1-10 pmoles/40 ul in assay buffer)

Add 10 μl compound or extract.

Add 10 μl ³² P!γ-ATP 10× stock.

Shake at 25° C. for 15 minutes.

Incubate additional 45 minutes at 25° C.

Stop the reaction by washing 4 times with 200 μl PBS.

Add 150 μl scintillation cocktail.

Count in Topcount.

D. Controls for all assays (located on each plate)

a. Non-specific binding

b. cold ATP at 80% inhibition.

2. Protocol for high throughput IKK-β-NIK binding assay

A. Reagents

Neutralite Avidin: 20 μg/ml in PBS.

Blocking buffer: 5% BSA, 0.5% Tween 20 in PBS; 1 hour at room temperature.

Assay Buffer: 100 mM KCl, 20 mM HEPES pH 7.6, 1 mM MgCl₂, 1% glycerol, 0.5% NP-40, 50 mM β-mercaptoethanol, 1 mg/ml BSA, cocktail of protease inhibitors.

³³ P IKK-β polypeptide 10× stock: 10⁻⁸ -10⁻⁶ M "cold" IKK-β supplemented with 200,000-250,000 cpm of labeled IKK-β (Beckman counter). Place in the 4° C. microfridge during screening.

Protease inhibitor cocktail (1000×): 10 mg Trypsin Inhibitor (BMB #109894), 10 mg Aprotinin (BMB #236624), 25 mg Benzamidine (Sigma #B-6506), 25 mg Leupeptin (BMB #1017128), 10 mg APMSF (BMB #917575), and 2 mM NaVO₃ (Sigma #S-6508) in 10 ml of PBS.

NIK: 10⁻⁷ -10⁻⁵ M biotinylated NIK in PBS.

B. Preparation of assay plates

Coat with 120 μl of stock N-Avidin per well overnight at 4° C.

Wash 2 times with 200 μl PBS.

Block with 150 μl of blocking buffer.

Wash 2 times with 200 μl PBS.

C. Assay

Add 40 μl assay buffer/well.

Add 10 μl compound or extract.

Add 10 μl ³³ P-EKK-β (20-25,000 cpm/0.1-10 pmoles/well=10⁻⁹ -10⁻⁷ M final conc).

Shake at 25° C. for 15 minutes.

Incubate additional 45 minutes at 25° C.

Add 40 μM biotinylated NIK (0.1-10 pmoles/40 ul in assay buffer)

Incubate 1 hour at room temperature.

Stop the reaction by washing 4 times with 200 μM PBS.

Add 150 μM scintillation cocktail.

Count in Topcount.

D. Controls for all assays (located on each plate)

a. Non-specific binding

b. Soluble (non-biotinylated NIK) at 80% inhibition.

All publications and patent applications cited in this specification are herein incorporated by reference as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference. Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be readily apparent to those of ordinary skill in the art in light of the teachings of this invention that certain changes and modifications may be made thereto without departing from the spirit or scope of the appended claims.

    __________________________________________________________________________     #             SEQUENCE LISTING     - (1) GENERAL INFORMATION:     -    (iii) NUMBER OF SEQUENCES: 4     - (2) INFORMATION FOR SEQ ID NO:1:     -      (i) SEQUENCE CHARACTERISTICS:     #pairs    (A) LENGTH: 2268 base               (B) TYPE: nucleic acid               (C) STRANDEDNESS: double               (D) TOPOLOGY: linear     -     (ii) MOLECULE TYPE: cDNA     -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1:     - ATGAGCTGGT CACCTTCCCT GACAACGCAG ACATGTGGGG CCTGGGAAAT GA - #AAGAGCGC       60     - CTTGGGACAG GGGGATTTGG AAATGTCATC CGATGGCACA ATCAGGAAAC AG - #GTGAGCAG      120     - ATTGCCATCA AGCAGTGCCG GCAGGAGCTC AGCCCCCGGA ACCGAGAGCG GT - #GGTGCCTG      180     - GAGATCCAGA TCATGAGAAG GCTGACCCAC CCCAATGTGG TGGCTGCCCG AG - #ATGTCCCT      240     - GAGGGGATGC AGAACTTGGC GCCCAATGAC CTGCCCCTGC TGGCCATGGA GT - #ACTGCCAA      300     - GGAGGAGATC TCCGGAAGTA CCTGAACCAG TTTGAGAACT GCTGTGGTCT GC - #GGGAAGGT      360     - GCCATCCTCA CCTTGCTGAG TGACATTGCC TCTGCGCTTA GATACCTTCA TG - #AAAACAGA      420     - ATCATCCATC GGGATCTAAA GCCAGAAAAC ATCGTCCTGC AGCAAGGAGA AC - #AGAGGTTA      480     - ATACACAAAA TTATTGACCT AGGATATGCC AAGGAGCTGG ATCAGGGCAG TC - #TTTGCACA      540     - TCATTCGTGG GGACCCTGCA GTACCTGGCC CCAGAGCTAC TGGAGCAGCA GA - #AGTACACA      600     - GTGACCGTCG ACTACTGGAG CTTCGGCACC CTGGCCTTTG AGTGCATCAC GG - #GCTTCCGG      660     - CCCTTCCTCC CCAACTGGCA GCCCGTGCAG TGGCATTCAA AAGTGCGGCA GA - #AGAGTGAG      720     - GTGGACATTG TTGTTAGCGA AGACTTGAAT GGAACGGTGA AGTTTTCAAG CT - #CTTTACCC      780     - TACCCCAATA ATCTTAACAG TGTCCTGGCT GAGCGACTGG AGAAGTGGCT GC - #AACTGATG      840     - CTGATGTGGC ACCCCCGACA GAGGGGCACG GATCCCACGT ATGGGCCCAA TG - #GCTGCTTC      900     - AAGGCCCTGG ATGACATCTT AAACTTAAAG CTGGTTCATA TCTTGAACAT GG - #TCACGGGC      960     - ACCATCCACA CCTACCCTGT GACAGAGGAT GAGAGTCTGC AGAGCTTGAA GG - #CCAGAATC     1020     - CAACAGGACA CGGGCATCCC AGAGGAGGAC CAGGAGCTGC TGCAGGAAGC GG - #GCCTGGCG     1080     - TTGATCCCCG ATAAGCCTGC CACTCAGTGT ATTTCAGACG GCAAGTTAAA TG - #AGGGCCAC     1140     - ACATTGGACA TGGATCTTGT TTTTCTCTTT GACAACAGTA AAATCACCTA TG - #AGACTCAG     1200     - ATCTCCCCAC GGCCCCAACC TGAAAGTGTC AGCTGTATCC TTCAAGAGCC CA - #AGAGGAAT     1260     - CTCGCCTTCT TCCAGCTGAG GAAGGTGTGG GGCCAGGTCT GGCACAGCAT CC - #AGACCCTG     1320     - AAGGAAGATT GCAACCGGCT GCAGCAGGGA CAGCGAGCCG CCATGATGAA TC - #TCCTCCGA     1380     - AACAACAGCT GCCTCTCCAA AATGAAGAAT TCCATGGCTT CCATGTCTCA GC - #AGCTCAAG     1440     - GCCAAGTTGG ATTTCTTCAA AACCAGCATC CAGATTGACC TGGAGAAGTA CA - #GCGAGCAA     1500     - ACCGAGTTTG GGATCACATC AGATAAACTG CTGCTGGCCT GGAGGGAAAT GG - #AGCAGGCT     1560     - GTGGAGCTCT GTGGGCGGGA GAACGAAGTG AAACTCCTGG TAGAACGGAT GA - #TGGCTCTG     1620     - CAGACCGACA TTGTGGACTT ACAGAGGAGC CCCATGGGCC GGAAGCAGGG GG - #GAACGCTG     1680     - GACGACCTAG AGGAGCAAGC AAGGGAGCTG TACAGGAGAC TAAGGGAAAA AC - #CTCGAGAC     1740     - CAGCGAACTG AGGGTGACAG TCAGGAAATG GTACGGCTGC TGCTTCAGGC AA - #TTCAGAGC     1800     - TTCGAGAAGA AAGTGCGAGT GATCTATACG CAGCTCAGTA AAACTGTGGT TT - #GCAAGCAG     1860     - AAGGCGCTGG AACTGTTGCC CAAGGTGGAA GAGGTGGTGA GCTTAATGAA TG - #AGGATGAG     1920     - AAGACTGTTG TCCGGCTGCA GGAGAAGCGG CAGAAGGAGC TCTGGAATCT CC - #TGAAGATT     1980     - GCTTGTAGCA AGGTCCGTGG TCCTGTCAGT GGAAGCCCGG ATAGCATGAA TG - #CCTCTCGA     2040     - CTTAGCCAGC CTGGGCAGCT GATGTCTCAG CCCTCCACGG CCTCCAACAG CT - #TACCTGAG     2100     - CCAGCCAAGA AGAGTGAAGA ACTGGTGGCT GAAGCACATA ACCTCTGCAC CC - #TGCTAGAA     2160     - AATGCCATAC AGGACACTGT GAGGGAACAA GACCAGAGTT TCACGGCCCT AG - #ACTGGAGC     2220     #              2268AAGA AGAGCACAGC TGCCTGGAGC AGGCCTCA     - (2) INFORMATION FOR SEQ ID NO:2:     -      (i) SEQUENCE CHARACTERISTICS:     #acids    (A) LENGTH: 756 amino               (B) TYPE: amino acid               (C) STRANDEDNESS: single               (D) TOPOLOGY: linear     -     (ii) MOLECULE TYPE: peptide     -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2:     - Met Ser Trp Ser Pro Ser Leu Thr Thr Gln Th - #r Cys Gly Ala Trp Glu     #                15     - Met Lys Glu Arg Leu Gly Thr Gly Gly Phe Gl - #y Asn Val Ile Arg Trp     #            30     - His Asn Gln Glu Thr Gly Glu Gln Ile Ala Il - #e Lys Gln Cys Arg Gln     #        45     - Glu Leu Ser Pro Arg Asn Arg Glu Arg Trp Cy - #s Leu Glu Ile Gln Ile     #    60     - Met Arg Arg Leu Thr His Pro Asn Val Val Al - #a Ala Arg Asp Val Pro     #80     - Glu Gly Met Gln Asn Leu Ala Pro Asn Asp Le - #u Pro Leu Leu Ala Met     #                95     - Glu Tyr Cys Gln Gly Gly Asp Leu Arg Lys Ty - #r Leu Asn Gln Phe Glu     #           110     - Asn Cys Cys Gly Leu Arg Glu Gly Ala Ile Le - #u Thr Leu Leu Ser Asp     #       125     - Ile Ala Ser Ala Leu Arg Tyr Leu His Glu As - #n Arg Ile Ile His Arg     #   140     - Asp Leu Lys Pro Glu Asn Ile Val Leu Gln Gl - #n Gly Glu Gln Arg Leu     145                 1 - #50                 1 - #55                 1 -     #60     - Ile His Lys Ile Ile Asp Leu Gly Tyr Ala Ly - #s Glu Leu Asp Gln Gly     #               175     - Ser Leu Cys Thr Ser Phe Val Gly Thr Leu Gl - #n Tyr Leu Ala Pro Glu     #           190     - Leu Leu Glu Gln Gln Lys Tyr Thr Val Thr Va - #l Asp Tyr Trp Ser Phe     #       205     - Gly Thr Leu Ala Phe Glu Cys Ile Thr Gly Ph - #e Arg Pro Phe Leu Pro     #   220     - Asn Trp Gln Pro Val Gln Trp His Ser Lys Va - #l Arg Gln Lys Ser Glu     225                 2 - #30                 2 - #35                 2 -     #40     - Val Asp Ile Val Val Ser Glu Asp Leu Asn Gl - #y Thr Val Lys Phe Ser     #               255     - Ser Ser Leu Pro Tyr Pro Asn Asn Leu Asn Se - #r Val Leu Ala Glu Arg     #           270     - Leu Glu Lys Trp Leu Gln Leu Met Leu Met Tr - #p His Pro Arg Gln Arg     #       285     - Gly Thr Asp Pro Thr Tyr Gly Pro Asn Gly Cy - #s Phe Lys Ala Leu Asp     #   300     - Asp Ile Leu Asn Leu Lys Leu Val His Ile Le - #u Asn Met Val Thr Gly     305                 3 - #10                 3 - #15                 3 -     #20     - Thr Ile His Thr Tyr Pro Val Thr Glu Asp Gl - #u Ser Leu Gln Ser Leu     #               335     - Lys Ala Arg Ile Gln Gln Asp Thr Gly Ile Pr - #o Glu Glu Asp Gln Glu     #           350     - Leu Leu Gln Glu Ala Gly Leu Ala Leu Ile Pr - #o Asp Lys Pro Ala Thr     #       365     - Gln Cys Ile Ser Asp Gly Lys Leu Asn Glu Gl - #y His Thr Leu Asp Met     #   380     - Asp Leu Val Phe Leu Phe Asp Asn Ser Lys Il - #e Thr Tyr Glu Thr Gln     385                 3 - #90                 3 - #95                 4 -     #00     - Ile Ser Pro Arg Pro Gln Pro Glu Ser Val Se - #r Cys Ile Leu Gln Glu     #               415     - Pro Lys Arg Asn Leu Ala Phe Phe Gln Leu Ar - #g Lys Val Trp Gly Gln     #           430     - Val Trp His Ser Ile Gln Thr Leu Lys Glu As - #p Cys Asn Arg Leu Gln     #       445     - Gln Gly Gln Arg Ala Ala Met Met Asn Leu Le - #u Arg Asn Asn Ser Cys     #   460     - Leu Ser Lys Met Lys Asn Ser Met Ala Ser Me - #t Ser Gln Gln Leu Lys     465                 4 - #70                 4 - #75                 4 -     #80     - Ala Lys Leu Asp Phe Phe Lys Thr Ser Ile Gl - #n Ile Asp Leu Glu Lys     #               495     - Tyr Ser Glu Gln Thr Glu Phe Gly Ile Thr Se - #r Asp Lys Leu Leu Leu     #           510     - Ala Trp Arg Glu Met Glu Gln Ala Val Glu Le - #u Cys Gly Arg Glu Asn     #       525     - Glu Val Lys Leu Leu Val Glu Arg Met Met Al - #a Leu Gln Thr Asp Ile     #   540     - Val Asp Leu Gln Arg Ser Pro Met Gly Arg Ly - #s Gln Gly Gly Thr Leu     545                 5 - #50                 5 - #55                 5 -     #60     - Asp Asp Leu Glu Glu Gln Ala Arg Glu Leu Ty - #r Arg Arg Leu Arg Glu     #               575     - Lys Pro Arg Asp Gln Arg Thr Glu Gly Asp Se - #r Gln Glu Met Val Arg     #           590     - Leu Leu Leu Gln Ala Ile Gln Ser Phe Glu Ly - #s Lys Val Arg Val Ile     #       605     - Tyr Thr Gln Leu Ser Lys Thr Val Val Cys Ly - #s Gln Lys Ala Leu Glu     #   620     - Leu Leu Pro Lys Val Glu Glu Val Val Ser Le - #u Met Asn Glu Asp Glu     625                 6 - #30                 6 - #35                 6 -     #40     - Lys Thr Val Val Arg Leu Gln Glu Lys Arg Gl - #n Lys Glu Leu Trp Asn     #               655     - Leu Leu Lys Ile Ala Cys Ser Lys Val Arg Gl - #y Pro Val Ser Gly Ser     #           670     - Pro Asp Ser Met Asn Ala Ser Arg Leu Ser Gl - #n Pro Gly Gln Leu Met     #       685     - Ser Gln Pro Ser Thr Ala Ser Asn Ser Leu Pr - #o Glu Pro Ala Lys Lys     #   700     - Ser Glu Glu Leu Val Ala Glu Ala His Asn Le - #u Cys Thr Leu Leu Glu     705                 7 - #10                 7 - #15                 7 -     #20     - Asn Ala Ile Gln Asp Thr Val Arg Glu Gln As - #p Gln Ser Phe Thr Ala     #               735     - Leu Asp Trp Ser Trp Leu Gln Thr Glu Glu Gl - #u Glu His Ser Cys Leu     #           750     - Glu Gln Ala Ser             755     - (2) INFORMATION FOR SEQ ID NO:3:     -      (i) SEQUENCE CHARACTERISTICS:     #pairs    (A) LENGTH: 2238 base               (B) TYPE: nucleic acid               (C) STRANDEDNESS: double               (D) TOPOLOGY: linear     -     (ii) MOLECULE TYPE: cDNA     -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO:3:     - ATGGAGCGGC CCCCGGGGCT GCGGCCGGGC GCGGGCGGGC CCTGGGAGAT GC - #GGGAGCGG       60     - CTGGGCACCG GCGGCTTCGG GAACGTCTGT CTGTACCAGC ATCGGGAACT TG - #ATCTCAAA      120     - ATAGCAATTA AGTCTTGTCG CCTAGAGCTA AGTACCAAAA ACAGAGAACG AT - #GGTGCCAT      180     - GAAATCCAGA TTATGAAGAA GTTGAACCAT GCCAATGTTG TAAAGGCCTG TG - #ATGTTCCT      240     - GAAGAATTGA ATATTTTGAT TCATGATGTG CCTCTTCTAG CAATGGAATA CT - #GTTCTGGA      300     - GGAGATCTCC GAAAGCTGCT CAACAAACCA GAAAATTGTT GTGGACTTAA AG - #AAAGCCAG      360     - ATACTTTCTT TACTAAGTGA TATAGGGTCT GGGATTCGAT ATTTGCATGA AA - #ACAAAATT      420     - ATACATCGAG ATCTAAAACC TGAAAACATA GTTCTTCAGG ATGTTGGTGG AA - #AGATAATA      480     - CATAAAATAA TTGATCTGGG ATATGCCAAA GATGTTGATC AAGGAAGTCT GT - #GTACATCT      540     - TTTGTGGGAA CACTGCAGTA TCTGGCCCCA GAGCTCTTTG AGAATAAGCC TT - #ACACAGCC      600     - ACTGTTGATT ATTGGAGCTT TGGGACCATG GTATTTGAAT GTATTGCTGG AT - #ATAGGCCT      660     - TTTTTGCATC ATCTGCAGCC ATTTACCTGG CATGAGAAGA TTAAGAAGAA GG - #ATCCAAAG      720     - TGTATATTTG CATGTGAAGA GATGTCAGGA GAAGTTCGGT TTAGTAGCCA TT - #TACCTCAA      780     - CCAAATAGCC TTTGTAGTTT AATAGTAGAA CCCATGGAAA ACTGGCTACA GT - #TGATGTTG      840     - AATTGGGACC CTCAGCAGAG AGGAGGACCT GTTGACCTTA CTTTGAAGCA GC - #CAAGATGT      900     - TTTGTATTAA TGGATCACAT TTTGAATTTG AAGATAGTAC ACATCCTAAA TA - #TGACTTCT      960     - GCAAAGATAA TTTCTTTTCT GTTACCACCT GATGAAAGTC TTCATTCACT AC - #AGTCTCGT     1020     - ATTGAGCGTG AAACTGGAAT AAATACTGGT TCTCAAGAAC TTCTTTCAGA GA - #CAGGAATT     1080     - TCTCTGGATC CTCGGAAACC AGCCTCTCAA TGTGTTCTAG ATGGAGTTAG AG - #GCTGTGAT     1140     - AGCTATATGG TTTATTTGTT TGATAAAAGT AAAACTGTAT ATGAAGGGCC AT - #TTGCTTCC     1200     - AGAAGTTTAT CTGATTGTGT AAATTATATT GTACAGGACA GCAAAATACA GC - #TTCCAATT     1260     - ATACAGCTGC GTAAAGTGTG GGCTGAAGCA GTGCACTATG TGTCTGGACT AA - #AAGAAGAC     1320     - TATAGCAGGC TCTTTCAGGG ACAAAGGGCA GCAATGTTAA GTCTTCTTAG AT - #ATAATGCT     1380     - AACTTAACAA AAATGAAGAA CACTTTGATC TCAGCATCAC AACAACTGAA AG - #CTAAATTG     1440     - GAGTTTTTTC ACAAAAGCAT TCAGCTTGAC TTGGAGAGAT ACAGCGAGCA GA - #TGACGTAT     1500     - GGGATATCTT CAGAAAAAAT GCTAAAAGCA TGGAAAGAAA TGGAAGAAAA GG - #CCATCCAC     1560     - TATGCTGAGG TTGGTGTCAT TGGATACCTG GAGGATCAGA TTATGTCTTT GC - #ATGCTGAA     1620     - ATCATGGAGC TACAGAAGAG CCCCTATGGA AGACGTCAGG GAGACTTGAT GG - #AATCTCTG     1680     - GAACAGCGTG CCATTGATCT ATATAAGCAG TTAAAACACA GACCTTCAGA TC - #ACTCCTAC     1740     - AGTGACAGCA CAGAGATGGT GAAAATCATT GTGCACACTG TGCAGAGTCA GG - #ACCGTGTG     1800     - CTCAAGGAGC TGTTTGGTCA TTTGAGCAAG TTGTTGGGCT GTAAGCAGAA GA - #TTATTGAT     1860     - CTACTCCCTA AGGTGGAAGT GGCCCTCAGT AATATCAAAG AAGCTGACAA TA - #CTGTCATG     1920     - TTCATGCAGG GAAAAAGGCA GAAAGAAATA TGGCATCTCC TTAAAATTGC CT - #GTACACAG     1980     - AGTTCTGCCC GGTCCCTTGT AGGATCCAGT CTAGAAGGTG CAGTAACCCC TC - #AGACATCA     2040     - GCATGGCTGC CCCCGACTTC AGCAGAACAT GATCATTCTC TGTCATGTGT GG - #TAACTCCT     2100     - CAAGATGGGG AGACTTCAGC ACAAATGATA GAAGAAAATT TGAACTGCCT TG - #GCCATTTA     2160     - AGCACTATTA TTCATGAGGC AAATGAGGAA CAGGGCAATA GTATGATGAA TC - #TTGATTGG     2220     #2238              GA     - (2) INFORMATION FOR SEQ ID NO:4:     -      (i) SEQUENCE CHARACTERISTICS:     #acids    (A) LENGTH: 745 amino               (B) TYPE: amino acid               (C) STRANDEDNESS: single               (D) TOPOLOGY: linear     -     (ii) MOLECULE TYPE: peptide     -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO:4:     - Met Glu Arg Pro Pro Gly Leu Arg Pro Gly Al - #a Gly Gly Pro Trp Glu     #                 15     - Met Arg Glu Arg Leu Gly Thr Gly Gly Phe Gl - #y Asn Val Cys Leu Tyr     #             30     - Gln His Arg Glu Leu Asp Leu Lys Ile Ala Il - #e Lys Ser Cys Arg Leu     #         45     - Glu Leu Ser Thr Lys Asn Arg Glu Arg Trp Cy - #s His Glu Ile Gln Ile     #     60     - Met Lys Lys Leu Asn His Ala Asn Val Val Ly - #s Ala Cys Asp Val Pro     # 80     - Glu Glu Leu Asn Ile Leu Ile His Asp Val Pr - #o Leu Leu Ala Met Glu     #                 95     - Tyr Cys Ser Gly Gly Asp Leu Arg Lys Leu Le - #u Asn Lys Pro Glu Asn     #           110     - Cys Cys Gly Leu Lys Glu Ser Gln Ile Leu Se - #r Leu Leu Ser Asp Ile     #       125     - Gly Ser Gly Ile Arg Tyr Leu His Glu Asn Ly - #s Ile Ile His Arg Asp     #   140     - Leu Lys Pro Glu Asn Ile Val Leu Gln Asp Va - #l Gly Gly Lys Ile Ile     145                 1 - #50                 1 - #55                 1 -     #60     - His Lys Ile Ile Asp Leu Gly Tyr Ala Lys As - #p Val Asp Gln Gly Ser     #               175     - Leu Cys Thr Ser Phe Val Gly Thr Leu Gln Ty - #r Leu Ala Pro Glu Leu     #           190     - Phe Glu Asn Lys Pro Tyr Thr Ala Thr Val As - #p Tyr Trp Ser Phe Gly     #       205     - Thr Met Val Phe Glu Cys Ile Ala Gly Tyr Ar - #g Pro Phe Leu His His     #   220     - Leu Gln Pro Phe Thr Trp His Glu Lys Ile Ly - #s Lys Lys Asp Pro Lys     225                 2 - #30                 2 - #35                 2 -     #40     - Cys Ile Phe Ala Cys Glu Glu Met Ser Gly Gl - #u Val Arg Phe Ser Ser     #               255     - His Leu Pro Gln Pro Asn Ser Leu Cys Ser Le - #u Ile Val Glu Pro Met     #           270     - Glu Asn Trp Leu Gln Leu Met Leu Asn Trp As - #p Pro Gln Gln Arg Gly     #       285     - Gly Pro Val Asp Leu Thr Leu Lys Gln Pro Ar - #g Cys Phe Val Leu Met     #   300     - Asp His Ile Leu Asn Leu Lys Ile Val His Il - #e Leu Asn Met Thr Ser     305                 3 - #10                 3 - #15                 3 -     #20     - Ala Lys Ile Ile Ser Phe Leu Leu Pro Pro As - #p Glu Ser Leu His Ser     #               335     - Leu Gln Ser Arg Ile Glu Arg Glu Thr Gly Il - #e Asn Thr Gly Ser Gln     #           350     - Glu Leu Leu Ser Glu Thr Gly Ile Ser Leu As - #p Pro Arg Lys Pro Ala     #       365     - Ser Gln Cys Val Leu Asp Gly Val Arg Gly Cy - #s Asp Ser Tyr Met Val     #   380     - Tyr Leu Phe Asp Lys Ser Lys Thr Val Tyr Gl - #u Gly Pro Phe Ala Ser     385                 3 - #90                 3 - #95                 4 -     #00     - Arg Ser Leu Ser Asp Cys Val Asn Tyr Ile Va - #l Gln Asp Ser Lys Ile     #               415     - Gln Leu Pro Ile Ile Gln Leu Arg Lys Val Tr - #p Ala Glu Ala Val His     #           430     - Tyr Val Ser Gly Leu Lys Glu Asp Tyr Ser Ar - #g Leu Phe Gln Gly Gln     #       445     - Arg Ala Ala Met Leu Ser Leu Leu Arg Tyr As - #n Ala Asn Leu Thr Lys     #   460     - Met Lys Asn Thr Leu Ile Ser Ala Ser Gln Gl - #n Leu Lys Ala Lys Leu     465                 4 - #70                 4 - #75                 4 -     #80     - Glu Phe Phe His Lys Ser Ile Gln Leu Asp Le - #u Glu Arg Tyr Ser Glu     #               495     - Gln Met Thr Tyr Gly Ile Ser Ser Glu Lys Me - #t Leu Lys Ala Trp Lys     #           510     - Glu Met Glu Glu Lys Ala Ile His Tyr Ala Gl - #u Val Gly Val Ile Gly     #       525     - Tyr Leu Glu Asp Gln Ile Met Ser Leu His Al - #a Glu Ile Met Glu Leu     #   540     - Gln Lys Ser Pro Tyr Gly Arg Arg Gln Gly As - #p Leu Met Glu Ser Leu     545                 5 - #50                 5 - #55                 5 -     #60     - Glu Gln Arg Ala Ile Asp Leu Tyr Lys Gln Le - #u Lys His Arg Pro Ser     #               575     - Asp His Ser Tyr Ser Asp Ser Thr Glu Met Va - #l Lys Ile Ile Val His     #           590     - Thr Val Gln Ser Gln Asp Arg Val Leu Lys Gl - #u Leu Phe Gly His Leu     #       605     - Ser Lys Leu Leu Gly Cys Lys Gln Lys Ile Il - #e Asp Leu Leu Pro Lys     #   620     - Val Glu Val Ala Leu Ser Asn Ile Lys Glu Al - #a Asp Asn Thr Val Met     625                 6 - #30                 6 - #35                 6 -     #40     - Phe Met Gln Gly Lys Arg Gln Lys Glu Ile Tr - #p His Leu Leu Lys Ile     #               655     - Ala Cys Thr Gln Ser Ser Ala Arg Ser Leu Va - #l Gly Ser Ser Leu Glu     #           670     - Gly Ala Val Thr Pro Gln Thr Ser Ala Trp Le - #u Pro Pro Thr Ser Ala     #       685     - Glu His Asp His Ser Leu Ser Cys Val Val Th - #r Pro Gln Asp Gly Glu     #   700     - Thr Ser Ala Gln Met Ile Glu Glu Asn Leu As - #n Cys Leu Gly His Leu     705                 7 - #10                 7 - #15                 7 -     #20     - Ser Thr Ile Ile His Glu Ala Asn Glu Glu Gl - #n Gly Asn Ser Met Met     #               735     - Asn Leu Asp Trp Ser Trp Leu Thr Glu     #           745     __________________________________________________________________________ 

What is claimed is:
 1. A method of screening for an agent which modulates the interaction of an IKKβ polypeptide to a binding target, the method comprising the steps of:incubating a mixture comprising:a polypeptide comprising at least 31 consecutive residues of the amino acid sequence set forth as SEQ ED NO:2, a binding target of the polypeptide, and a candidate agent; under conditions whereby, but for the presence of the agent, the polypeptide specifically binds said binding target at a reference affinity; detecting the binding affinity of the polypeptide to the binding target to determine an agent-biased affinity, wherein a difference between the agent-biased affinity and the reference affinity indicates that the agent modulates the binding of the polypeptide to the binding target.
 2. A method according to claim 1, wherein the polypeptide comprises the amino acid sequence set forth as SEQ ID NO:2.
 3. A method according to claim 1, wherein the polypeptide is made by a method comprising the steps of:introducing a recombinant nucleic acid encoding a polypeptide comprising at least 31 consecutive residues of the amino acid sequence set forth as SEQ ID NO:2 into a host cell or cellular extract; and incubating the host cell or cellular extract under conditions whereby the polypeptide is expressed.
 4. A method according to claim 1, wherein the polypeptide is made by a method comprising the steps of:introducing a recombinant nucleic acid comprising SEQ ID NO:1 or a fragment thereof sufficient to encode a polypeptide comprising at least 31 consecutive residues of the amino acid sequence set forth as SEQ ID NO:2 into a host cell or cellular extract; and incubating the host cell or cellular extract under conditions whereby the polypeptide is expressed.
 5. A method according to claim 1, wherein the polypeptide is made by a method comprising the steps ofintroducing a recombinant nucleic acid encoding a polypeptide comprising the amino acid sequence set forth as SEQ ID NO:2 into a host cell or cellular extract; and incubating the host cell or cellular extract under conditions whereby the polypeptide is expressed.
 6. A method according to claim 1, wherein the polypeptide is made by a method comprising the steps of:introducing a recombinant nucleic acid comprising SEQ ID NO:1 or a fragment thereof sufficient to encode a polypeptide comprising the amino acid sequence set forth as SEQ ID NO:2 into a host cell or cellular extract; and incubating the host cell or cellular extract under conditions whereby the polypeptide is expressed.
 7. A method according to claim 1 wherein the binding target comprises an IκB polypeptide domain.
 8. A method according to claim 1 wherein the binding target comprises an IKK polypeptide domain.
 9. A method according to claim 1 wherein the binding target comprises a NIK polypeptide domain.
 10. A method according to claim 1, wherein the binding target is a natural intracellular substrate and the reference and agent-biased binding affinity is detected as phosphorylation of the substrate.
 11. A method according to claim 10 wherein the substrate comprises a IκB polypeptide domain.
 12. A method according to claim 10 wherein the substrate comprises a IκB polypeptide domain comprising at least one of serine 32 and serine 36, and at least five naturally occurring immediately flanking residues.
 13. A method according to claim 10 wherein the substrate comprises a IκB polypeptide domain.
 14. A method according to claim 10 wherein the substrate is biotinylated and the detecting step comprises capturing the substrate on an avidin-coated surface.
 15. A method according to claim 10 wherein the mixture further comprises ATP having a labeled phosphate and the detecting step comprises detecting the presence of the labeled phosphate on the substrate.
 16. A method according to claim 10 wherein the phosphorylation of the substrate is detected with an antibody. 